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NM_000368.4(TSC1):c.2115G>A (p.Glu705=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000207614.6
Variation ID:
207614
Description:
single nucleotide variant
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NM_000368.4(TSC1):c.2115G>A (p.Glu705=)

Allele ID
202477
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 132903744 (GRCh38) GRCh38 UCSC
9: 135779131 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_486:g.45890G>A
LRG_486t1:c.2115G>A LRG_486p1:p.Glu705=
NC_000009.11:g.135779131C>T
... more HGVS
Protein change
-
Other names
p.E705E:GAG>GAA
Canonical SPDI
NC_000009.12:132903743:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA031535
dbSNP: rs142662480
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jul 24, 2014 RCV000189818.1
Likely benign 1 criteria provided, single submitter Sep 4, 2015 RCV000718497.1
Uncertain significance 1 criteria provided, single submitter Apr 16, 2018 RCV000732642.3
Likely benign 1 criteria provided, single submitter Dec 4, 2020 RCV001081924.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TSC1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2790 2834

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 24, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000243470.11
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Tuberous sclerosis 1
Allele origin: germline
Invitae
Accession: SCV000562476.6
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Apr 16, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000860617.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Sep 04, 2015)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000849361.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TSC1 - - - -

Text-mined citations for rs142662480...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021